Maelstrom Pulse has only one target. If that permanent is an illegal target as Maelstrom Pulse tries to resolve, it will be countered and none of its effects will happen. Nothing will be destroyed.

5/1/2009

The name of a creature token is the same as its creature types unless the token is a copy of another creature or the effect that created the token specifically gives it a different name. For example, a 1/1 Soldier creature token is named “Soldier.”

5/1/2009

A face-down creature has no name, so it doesn't have the same name as anything else.

7/1/2013

If Maelstrom Pulse resolves but the targeted permanent isn't destroyed (perhaps because it regenerates or has indestructible), all other permanents with the same name as it will still be destroyed (unless they also have indestructible.